subOTUset {OTUbase} | R Documentation |
Function to get a subset of an OTUset object.
subOTUset(object, samples, otus)
object |
An OTUset object |
samples |
A list of sample names |
otus |
A list of OTU names |
subOTUset
returns an OTUset
## locate directory with data dirPath <- system.file("extdata/Sogin_2006", package="OTUbase") ## read in data into OTUset object soginOTU <- readOTUset(dirPath=dirPath, level="0.03", samplefile="sogin.groups", fastafile="sogin.fasta", otufile="sogin.unique.filter.fn.list", sampleADF="sample_metadata.txt") ## get subset of soginOTU subOTUset(soginOTU, samples=getSamples(soginOTU, colnum="Site", value="Labrador", exact=FALSE))